bph genes of the thermophilic PCB degrader, Bacillus sp. JF8: characterization of the divergent ring-hydroxylating dioxygenase and hydrolase genes upstream of the Mn-dependent BphC

Mukerjee-Dhar, Gouri; Shimura, Minoru; Miyazawa, Daisuke; Kimbara, Kazuhide; Hatta, Takashi

doi:10.1099/mic.0.28437-0

Cited by 37 publications

(16 citation statements)

References 76 publications

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“…Six gene pairs in region A, Mvan_0463/0464 (phtAaAb), 0487/0488 (nidAB), 0525/0526 (nidA3B3), 0533/0534, 0539/0540, and 0546/0547, have been previously identified to be involved in aromatic hydrocarbon degradation (Khan et al 2001;Stingley et al 2004;Kim et al 2006Kim et al , 2007Kweon et al 2007). Sequence analysis indicated that Mvan_0546/0547 also likely transforms other PAHs including phenanthrene, naphthalene, and biphenyl because it contains a considerable sequence similarity to other enzymes having such substrate specificities (Larkin et al 1999;Mukerjee-Dhar et al 2005). The seventh RHO pair in region A, Mvan_0492/0493 is similar to the salicylate hydroxylase from Sphingomonas sp.…”

Section: Genes Involved In the Upper Pathway Of Pah Degradationmentioning

confidence: 96%

Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1

et al. 2008

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Mycobacterium vanbaalenii PYR-1 is well known for its ability to degrade a wide range of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs). The genome of this bacterium has recently been sequenced, allowing us to gain insights into the molecular basis for the degradation of PAHs. The 6.5 Mb genome of PYR-1 contains 194 chromosomally encoded genes likely associated with degradation of aromatic compounds. The most distinctive feature of the genome is the presence of a 150 kb major catabolic region at positions 494 approximately 643 kb (region A), with an additional 31 kb region at positions 4,711 approximately 4,741 kb (region B), which is predicted to encode most enzymes for the degradation of PAHs. Region A has an atypical mosaic structure made of several gene clusters in which the genes for PAH degradation are complexly arranged and scattered around the clusters. Significant differences in the gene structure and organization as compared to other well-known aromatic hydrocarbon degraders including Pseudomonas and Burkholderia were revealed. Many identified genes were enriched with multiple paralogs showing a remarkable range of diversity, which could contribute to the wide variety of PAHs degraded by M. vanbaalenii PYR-1. The PYR-1 genome also revealed the presence of 28 genes involved in the TCA cycle. Based on the results, we proposed a pathway in which HMW PAHs are degraded into the beta-ketoadipate pathway through protocatechuate and then mineralized to CO2 via TCA cycle. We also identified 67 and 23 genes involved in PAH degradation and TCA cycle pathways, respectively, to be expressed as proteins.

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Section: Genes Involved In the Upper Pathway Of Pah Degradationmentioning

confidence: 96%

Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1

et al. 2008

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“…Although the annotation of BphD JF8 from Bacillus sp. strain JF8 (25) suggests that this class III enzyme is involved in biphenyl catabolism, the ringhydroxylating dioxygenase encoded by the operon containing bphD JF8 is most closely related to enzymes that catalyze angular dioxygenation, strongly suggesting that the natural substrate of BphD JF8 is also an ortho-substituted HOPDA. The third putative MCP hydrolase of S. wittichii RW1 (2), encoded by orfG7, is evolutionarily divergent from other MCP hydrolases.…”

Section: Methodsmentioning

confidence: 99%

Characterization of a C—C Bond Hydrolase fromSphingomonas wittichiiRW1 with Novel Specificities towards Polychlorinated Biphenyl Metabolites

Seah

Denis

et al. 2007

J Bacteriol

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Sphingomonas wittichii RW1 degrades chlorinated dibenzofurans and dibenzo-p-dioxins via meta cleavage. We used inverse PCR to amplify dxnB2, a gene encoding one of three meta-cleavage product (MCP) hydrolases identified in the organism that are homologues of BphD involved in biphenyl catabolism. Purified DxnB2 catalyzed the hydrolysis of 8-OH 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (HOPDA) approximately six times faster than for HOPDA at saturating substrate concentrations. Moreover, the specificity of DxnB2 for HOPDA (k cat /K m ‫؍‬ 1.2 ؋ 10 7 M ؊1 s ؊1 ) was about half that of the BphDs of Burkholderia xenovorans LB400 and Rhodococcus globerulus P6, two potent polychlorinated biphenyl (PCB)-degrading strains. Interestingly, DxnB2 transformed 3-Cl and 4-OH HOPDAs, compounds that inhibit the BphDs and limit PCB degradation. DxnB2 had a higher specificity for 9-Cl HOPDA than for HOPDA but a lower specificity for 8-Cl HOPDA (k cat /K m ‫؍‬ 1.7 ؋ 10 6 M ؊1 s ؊1 ), the chlorinated analog of 8-OH HOPDA produced during dibenzofuran catabolism. Phylogenetic analyses based on structure-guided sequence alignment revealed that DxnB2 belongs to a previously unrecognized class of MCP hydrolases, evolutionarily divergent from the BphDs although the physiological substrates of both enzyme types are HOPDAs. However, both classes of enzymes have mainly small hydrophobic residues lining the subsite that binds the C-6 phenyl of HOPDA, in contrast to the bulky hydrophobic residues (Phe106, Phe135, Trp150, and Phe197) found in the class II enzymes that prefer substrates possessing a C-6 alkyl. Thr196 and/or Asn203 appears to be an important determinant of specificity for DxnB2, potentially forming hydrogen bonds with the 8-OH substituent. This study demonstrates that the substrate specificities of evolutionarily divergent hydrolases may be useful for degrading mixtures of pollutants, such as PCBs.Chlorinated aromatic compounds, such as polychlorinated biphenyls (PCBs) and dibenzofurans, are among the most widespread, toxic, and/or persistent environmental pollutants. The Bph and Dxn/Dbf pathways responsible for the aerobic bacterial catabolism of biphenyl and dibenzofuran, respectively, have been extensively studied, in part due to their potential for remediating environments contaminated with the polychlorinated compounds (2, 10). The pathways share three homologous enzymes ( Fig. 1): a multicomponent dioxygenase that catalyzes the initial step of ring hydroxylation, an extradiol dioxygenase that catalyzes oxygenolytic cleavage of the catecholic intermediate at the meta position to yield 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (HOPDA) or ortho-substituted HOPDA, and a metacleavage product (MCP) hydrolase that catalyzes an unusual COC bond cleavage of the HOPDA.A general limitation of bacterial catabolic pathways for the degradation of complex industrial mixtures is that one or more pathway enzymes lack the requisite broad substrate specificity to degrade all man-made (xenobiotic) congeners of the naturally occurring compounds,...

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“…Also, the Mn(II)-dependent BphC and BphD ( fig. 4 ) evidently belong to new subfamilies in the phylogeny of extradiol dioxygenases and hydrolases acting on extradiol cleavage products [Hatta et al, 2003;Mukerjee-Dhar et al, 2005].…”

Section: Metabolic Versatilitymentioning

confidence: 99%

“…The bph operon of Bacillus sp. JF8 harbors a novel bphRDA1A2BC cluster [Mukerjee-Dhar et al, 2005] ( fig. 3 ) encoding enzymes only distantly related to enzymes previously described to be important for biphenyl degradation ( fig.…”

Section: Metabolic Versatilitymentioning

confidence: 99%

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Bacterial Metabolism of Polychlorinated Biphenyls

2008

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Microbial metabolism is responsible for the removal of persistent organic pollutants including PCBs from the environment. Anaerobic dehalogenation of highly chlorinated congeners in aquatic sediments is an important process, and recent evidence has indicated that Dehalococcoides and related organisms are predominantly responsible for this process. Such anaerobic dehalogenation generates lower chlorinated congeners which are easily degraded aerobically by enzymes of the biphenyl upper pathway (bph). Initial biphenyl 2,3-dioxygenases are generally considered the key enzymes of this pathway which determine substrate range and extent of PCB degradation. These enzymes have been subject to different protein evolution strategies, and subsequent enzymes have been considered as crucial for metabolism. Significant advances have been made regarding the mechanistic understanding of these enzymes, which has also included elucidation of the function of BphK glutathione transferase. So far, the genomes of two important PCB-metabolizing organisms, namely Burkholderia xenovorans strain LB400 and Rhodococcus sp. strain RHA1, have been sequenced, with the rational to better understand their overall physiology and evolution. Genomic and proteomic analysis also allowed a better evaluation of PCB toxicity. Like all bph gene clusters which have been characterized in detail, particularly in strains LB400 and RHA1, these genes were localized on mobile genetic elements endowing single strains and microbial communities with a high flexibility and adaptability. However, studies show that our knowledge on enzymes and genes involved in PCB metabolism is still rather fragmentary and that the diversity of bacterial strategies is highly underestimated. Overall, metabolism of biphenyl and PCBs should not be regarded as a simple linear pathway, but as a complex interplay between different catabolic gene modules.

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bph genes of the thermophilic PCB degrader, Bacillus sp. JF8: characterization of the divergent ring-hydroxylating dioxygenase and hydrolase genes upstream of the Mn-dependent BphC

Cited by 37 publications

References 76 publications

Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1

Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1

Characterization of a C—C Bond Hydrolase fromSphingomonas wittichiiRW1 with Novel Specificities towards Polychlorinated Biphenyl Metabolites

Bacterial Metabolism of Polychlorinated Biphenyls

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